STRait Razor v2s

Advancing sequence-based STR allele reporting and beyond to other marker systems

Jonathan L. King, Frank R. Wendt, Jie Sun, Bruce Budowle

Research output: Contribution to journalArticleResearchpeer-review

16 Citations (Scopus)

Abstract

STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and “early access” panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e.g., vWA allele 14), and International Society of Forensic Genetics (ISFG)-recommended (vWA [CE 14]-GRCh38-chr12:5983950-5984049 (TAGA)10 (CAGA)3 TAGA) formats. STRait Razor v2s currently contains a database of ∼2500 unique sequences. This database is used by SRv2s to match strings to the appropriate allele in ISFG-recommended format. In addition to STRs, SRv2s has configuration files necessary to capture and report haplotypes from all marker types included in these multiplexes (e.g., SNPs, InDels, and microhaplotypes). To facilitate mixture interpretation, data may be displayed from all markers in a format similar to that of electropherograms displayed by traditional forensic software. The download package for SRv2s may be found at https://www.unthsc.edu/graduate-school-of-biomedical-sciences/molecular-and-medical-genetics/laboratory-faculty-and-staff/strait-razor.

Original languageEnglish
Pages (from-to)21-28
Number of pages8
JournalForensic Science International: Genetics
Volume29
DOIs
StatePublished - 1 Jul 2017

Fingerprint

Forensic Genetics
Microsatellite Repeats
Haplotypes
Alleles
Databases
High-Throughput Nucleotide Sequencing
Medical Genetics
Single Nucleotide Polymorphism
Molecular Biology
Software
Population

Keywords

  • Bioinformatics
  • Massively parallel sequencing
  • Microhaplotypes
  • SNPs
  • STRait Razor
  • Short tandem repeat

Cite this

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title = "STRait Razor v2s: Advancing sequence-based STR allele reporting and beyond to other marker systems",
abstract = "STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and “early access” panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e.g., vWA allele 14), and International Society of Forensic Genetics (ISFG)-recommended (vWA [CE 14]-GRCh38-chr12:5983950-5984049 (TAGA)10 (CAGA)3 TAGA) formats. STRait Razor v2s currently contains a database of ∼2500 unique sequences. This database is used by SRv2s to match strings to the appropriate allele in ISFG-recommended format. In addition to STRs, SRv2s has configuration files necessary to capture and report haplotypes from all marker types included in these multiplexes (e.g., SNPs, InDels, and microhaplotypes). To facilitate mixture interpretation, data may be displayed from all markers in a format similar to that of electropherograms displayed by traditional forensic software. The download package for SRv2s may be found at https://www.unthsc.edu/graduate-school-of-biomedical-sciences/molecular-and-medical-genetics/laboratory-faculty-and-staff/strait-razor.",
keywords = "Bioinformatics, Massively parallel sequencing, Microhaplotypes, SNPs, STRait Razor, Short tandem repeat",
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STRait Razor v2s : Advancing sequence-based STR allele reporting and beyond to other marker systems. / King, Jonathan L.; Wendt, Frank R.; Sun, Jie; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 29, 01.07.2017, p. 21-28.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Wendt, Frank R.

AU - Sun, Jie

AU - Budowle, Bruce

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KW - Microhaplotypes

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